I did Belawan (Sumatra) - Java - Bali in just about 1 month in Feb-08, and it was quite wet at times, especially in eastern Java, with some road closures (and ´interesting´ riding in something, that looks more like a river than a road!) Northern & central Sumatra wasn´t so rainy. And in Bali it seemed to rain mostly after dark (but maybe we were just lucky). Java was the only place, where the rain seemed more constant. Low-lying areas may flood, and in the mountain roads you have the possibility of landslides.
So yeah, at that time you´ll probably get some rain, or even quite a bit, somewhere along the way... but I still would not skip Indonesia, it was one of the most fascinating places that I´ve ever been to!
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